Paper Citation Record · LEDGER

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates

As of 15 August 2026, this Paper Citation Record lists 46 of 46 outbound references and 1 inbound Pith citation observation for arXiv:2412.01564.

A citation records a reference. It does not transfer a finding from one paper to another.

pith.paper-citation-record.v1
2412.01564 v1

Coverage vector

measured 46 of 46 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-12T04:21:50.182500Z

measured 47 of 47 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-15T06:32:42.880941+00:00

measured 1 of 1 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links, observed 2026-08-01T22:02:30.814826Z

measured 0 of 1 external citation measurements

A source-named dated measurement, never combined with another source.

Source: cited_works

Reference resolution

46 of 46 outbound references displayed

verified exact2
verified fuzzy27
unresolved17
parse uncertain0
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External citation measurements

No source-named external measurement is stored.

Outbound references

Observation 655df9ac-2674-479a-a189-8db46e556320 · outbound

This paper cites PoseBusters : AI -based docking methods fail to generate physically valid poses or generalise to novel sequences.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates PoseBusters : AI -based docking methods fail to generate physically valid poses or generalise to novel sequences

Reference 1

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.814850Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 1e545142-5383-49e7-baa6-5adb27f964f8 · outbound

This paper cites Symphony: S ymmetry-equivariant point-centered spherical harmonics for 3D molecule generation.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Symphony: S ymmetry-equivariant point-centered spherical harmonics for 3D molecule generation

Reference 2

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.800564Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation a148b853-67ae-4891-a398-47b1681d856c · outbound

This paper cites Neural scaling of deep chemical models.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Neural scaling of deep chemical models

Reference 3

Resolution: unresolved; no resolver link, observed 2026-08-12T04:21:49.979726Z

Source-reported events for the cited work

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Observation a0972c9c-5caa-40f3-b43c-b62e51208a65 · outbound

This paper cites FoldToken: Learning Protein Language via Vector Quantization and Beyond.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates FoldToken: Learning Protein Language via Vector Quantization and Beyond

Reference 4

Resolution: verified exact; local_arxiv, observed 2026-08-12T04:21:50.305511Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 8fa5949f-19a5-4c73-8de7-7d137b68a814 · outbound

This paper cites E (n) equivariant normalizing flows.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates E (n) equivariant normalizing flows

Reference 5

Resolution: unresolved; no resolver link, observed 2026-08-12T04:21:49.990522Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 4ef52910-c3da-4cfb-bac2-66a696f497d8 · outbound

This paper cites Symmetry-adapted generation of 3D point sets for the targeted discovery of molecules.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Symmetry-adapted generation of 3D point sets for the targeted discovery of molecules

Reference 6

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.765975Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 8df1ff81-1bf8-4477-b683-03af8e63e85d · outbound

This paper cites Neural message passing for quantum chemistry.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Neural message passing for quantum chemistry

Reference 7

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.750281Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 61d019a3-82ff-4088-ab2d-3676525b0062 · outbound

This paper cites xVal: A Continuous Numerical Tokenization for Scientific Language Models.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates xVal: A Continuous Numerical Tokenization for Scientific Language Models

Reference 8

Resolution: unresolved; no resolver link, observed 2026-08-12T04:21:50.005681Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation d12b1ce7-23f3-424b-8efc-f00368401897 · outbound

This paper cites Simulating 500 million years of evolution with a language model.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Simulating 500 million years of evolution with a language model

Reference 9

Resolution: unresolved; no resolver link, observed 2026-08-12T04:21:50.010735Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 260ba7bb-5a0f-44ec-a4cd-f9141407339b · outbound

This paper cites Bilingual language model for protein sequence and structure.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Bilingual language model for protein sequence and structure

Reference 10

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.725835Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 8fa8aaaf-71f5-404e-9a21-3b8cf5f246a3 · outbound

This paper cites Equivariant diffusion for molecule generation in 3D.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Equivariant diffusion for molecule generation in 3D

Reference 11

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.711351Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 26f181a0-ab2f-4e78-b366-f860e44d3c16 · outbound

This paper cites Chemformer: a pre-trained transformer for computational chemistry.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Chemformer: a pre-trained transformer for computational chemistry

Reference 12

Resolution: unresolved; no resolver link, observed 2026-08-12T04:21:50.024608Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 3a11fbe5-14d0-4fdb-8647-fce2f3cee727 · outbound

This paper cites Universal structure conversion method for organic molecules: F rom atomic connectivity to three-dimensional geometry.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Universal structure conversion method for organic molecules: F rom atomic connectivity to three-dimensional geometry

Reference 13

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.687668Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation e997142a-42e8-46e8-a617-b047cc246d9f · outbound

This paper cites Self-referencing embedded strings ( SELFIES ): A 100\ Machine Learning: Science and Technology, 1 0 (4): 0 045024, 2020.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Self-referencing embedded strings ( SELFIES ): A 100\ Machine Learning: Science and Technology, 1 0 (4): 0 045024, 2020

Reference 14

Resolution: unresolved; no resolver link, observed 2026-08-12T04:21:50.033606Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation eac12ff5-4383-4c6d-a685-9634865e89cd · outbound

This paper cites Geometry Informed Tokenization of Molecules for Language Model Generation.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Geometry Informed Tokenization of Molecules for Language Model Generation

Reference 15

Resolution: unresolved; no resolver link, observed 2026-08-12T04:21:50.038328Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation d997665f-86c0-4d5a-8433-8e823ef5c25e · outbound

This paper cites Nach0 : Multimodal natural and chemical languages foundation model.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Nach0 : Multimodal natural and chemical languages foundation model

Reference 16

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.663095Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 0ae20f9d-8f04-4e38-9992-ad02a9717eee · outbound

This paper cites One transformer can understand both 2D & 3D molecular data.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates One transformer can understand both 2D & 3D molecular data

Reference 17

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.650082Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 89b26fae-f48d-4d92-9f3f-a87863f9c5b9 · outbound

This paper cites An autoregressive flow model for 3D molecular geometry generation from scratch.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates An autoregressive flow model for 3D molecular geometry generation from scratch

Reference 18

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.636403Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation cee5d514-47c8-465e-b2dc-8ebfdab6b02a · outbound

This paper cites GraphDF : A discrete flow model for molecular graph generation.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates GraphDF : A discrete flow model for molecular graph generation

Reference 19

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.622653Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation fba906cb-3421-4d5c-a980-8fa1adcf9f89 · outbound

This paper cites PubChemQC project: A large-scale first-principles electronic structure database for data-driven chemistry.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates PubChemQC project: A large-scale first-principles electronic structure database for data-driven chemistry

Reference 20

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.608282Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 7a115524-5f4d-482b-b2e6-d191f181b32a · outbound

This paper cites 3DMolNet: A Generative Network for Molecular Structures.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates 3DMolNet: A Generative Network for Molecular Structures

Reference 21

Resolution: verified exact; local_arxiv, observed 2026-08-12T04:21:50.256243Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 7045aebd-a842-4990-aca4-4e891c47bf07 · outbound

This paper cites Open Babel : A n open chemical toolbox.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Open Babel : A n open chemical toolbox

Reference 22

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.594594Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 36af6d78-da09-4ebc-a69b-445ae5490b49 · outbound

This paper cites MolecularRNN: Generating realistic molecular graphs with optimized properties.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates MolecularRNN: Generating realistic molecular graphs with optimized properties

Reference 23

Resolution: unresolved; no resolver link, observed 2026-08-12T04:21:50.076435Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation dbc324ec-f0a9-42f9-9057-5a229539c91c · outbound

This paper cites Language models are unsupervised multitask learners.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Language models are unsupervised multitask learners

Reference 24

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.580554Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation c0b6b029-d270-4de9-849f-62388f48e8fc · outbound

This paper cites Quantum chemistry structures and properties of 134 kilo molecules.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Quantum chemistry structures and properties of 134 kilo molecules

Reference 25

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.566266Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 5f6b8be6-eb80-4aeb-bbed-da62d464982d · outbound

This paper cites Zero-shot text-to-image generation.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Zero-shot text-to-image generation

Reference 26

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.550938Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation d4d10c9d-bd51-495e-80f7-41b64549f43d · outbound

This paper cites Generating diverse high-fidelity images with VQ-VAE-2.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Generating diverse high-fidelity images with VQ-VAE-2

Reference 27

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.536830Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation a34d9fa4-e26a-4ec4-8188-1e437e3da703 · outbound

This paper cites E (n) equivariant graph neural networks.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates E (n) equivariant graph neural networks

Reference 28

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.522868Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 52690efa-e43e-4f56-a715-6bd604bb1a08 · outbound

This paper cites u tt, Huziel E Sauceda, P-J Kindermans, Alexandre Tkatchenko, and K-R M \.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates u tt, Huziel E Sauceda, P-J Kindermans, Alexandre Tkatchenko, and K-R M \

Reference 29

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.507392Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation aa4af554-d25f-4b6f-8a20-8e37f8e2a452 · outbound

This paper cites GraphAF : A flow-based autoregressive model for molecular graph generation.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates GraphAF : A flow-based autoregressive model for molecular graph generation

Reference 30

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.493071Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 94039036-a75c-4fcc-9e0f-bbb57fb45b6c · outbound

This paper cites Reinforcement learning for molecular design guided by quantum mechanics.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Reinforcement learning for molecular design guided by quantum mechanics

Reference 31

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.478081Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 6f57d079-1e58-4c94-a647-e92a13479bf3 · outbound

This paper cites Unified generative modeling of 3D molecules via bayesian flow networks.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Unified generative modeling of 3D molecules via bayesian flow networks

Reference 32

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.463395Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 6b909e90-3537-414c-a392-4385bcb60cb4 · outbound

This paper cites SaProt : Protein language modeling with structure-aware vocabulary.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates SaProt : Protein language modeling with structure-aware vocabulary

Reference 33

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.449588Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation f2ae622b-818e-4805-aaff-2e98f7a58b75 · outbound

This paper cites Neural discrete representation learning.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Neural discrete representation learning

Reference 34

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Source-reported events for the cited work

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Observation b7b6aa61-d8fd-4ec7-b8a6-382e5956ceac · outbound

This paper cites Gilchrist, Johannes S \"o ding, and Martin Steinegger.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Gilchrist, Johannes S \"o ding, and Martin Steinegger

Reference 35

Resolution: unresolved; no resolver link, observed 2026-08-12T04:21:50.132270Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 898077c0-96fb-4094-af19-a0e85041165b · outbound

This paper cites Attention is all you need.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Attention is all you need

Reference 36

Resolution: unresolved; no resolver link, observed 2026-08-12T04:21:50.136445Z

Source-reported events for the cited work

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Observation b5b409ec-25f8-4c07-b576-cd1fc9520d6a · outbound

This paper cites SMILES , a chemical language and information system.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates SMILES , a chemical language and information system

Reference 37

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.407226Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation ccf47456-c64b-4b22-b495-fd88eb87e91b · outbound

This paper cites Geometric latent diffusion models for 3D molecule generation.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Geometric latent diffusion models for 3D molecule generation

Reference 38

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.392915Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 6fa65341-ce00-42ba-a52f-c4de191ed6d7 · outbound

This paper cites Do transformers really perform badly for graph representation? Advances in Neural Information Processing Systems, 34: 0 28877--28888, 2021.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Do transformers really perform badly for graph representation? Advances in Neural Information Processing Systems, 34: 0 28877--28888, 2021

Reference 39

Resolution: unresolved; no resolver link, observed 2026-08-12T04:21:50.147971Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation fd9f166b-3864-4774-b1cf-f1864250c4b4 · outbound

This paper cites Latent 3D graph diffusion.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Latent 3D graph diffusion

Reference 40

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.368762Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation da39ea7b-c53c-4d68-ba63-3a6839793f9b · outbound

This paper cites An equivariant generative framework for molecular graph-structure co-design.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates An equivariant generative framework for molecular graph-structure co-design

Reference 41

Resolution: verified fuzzy; raw_fallback, observed 2026-08-12T04:21:50.354841Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

Observation 681828b9-b636-4a28-b79f-b02add80bc4f · outbound

This paper cites BindGPT: A Scalable Framework for 3D Molecular Design via Language Modeling and Reinforcement Learning.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates BindGPT: A Scalable Framework for 3D Molecular Design via Language Modeling and Reinforcement Learning

Reference 42

Resolution: unresolved; no resolver link, observed 2026-08-12T04:21:50.161518Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 3d93095b-909c-44b5-92d3-1b22789a6b67 · outbound

This paper cites write newline.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates write newline

Reference 43

Resolution: unresolved; no resolver link, observed 2026-08-12T04:21:50.166165Z

Source-reported events for the cited work

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Observation 4e6c4ca9-1663-4c3c-9697-69bfbfbb41b6 · outbound

This paper cites @esa (Ref.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates @esa (Ref

Reference 44

Resolution: unresolved; no resolver link, observed 2026-08-12T04:21:50.172746Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation e2865cd7-bdb4-41a6-a1a8-fb35134f5b9e · outbound

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Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Unresolved cited work

Reference 45

Resolution: unresolved; no resolver link, observed 2026-08-12T04:21:50.177285Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 41530dcd-39d1-47ce-883a-4b4bca37e685 · outbound

This paper cites an unresolved cited work.

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates Unresolved cited work

Reference 46

Resolution: unresolved; no resolver link, observed 2026-08-12T04:21:50.182500Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Pith citing papers

Observation d3324416-e5cb-4c72-9f1f-731a1b96b24f · inbound

Atomic Design Transformer: Scaffold-Conditioned 3D Molecule Generation via xTB-Reward Reinforcement Learning cites this paper.

Atomic Design Transformer: Scaffold-Conditioned 3D Molecule Generation via xTB-Reward Reinforcement Learning Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates

Reference 18

Resolution: unresolved; no resolver link, observed 2026-08-01T22:02:30.814826Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.